florets {SpatialDecon} | R Documentation

## Draw coxcomb plots as points in a graphics window

### Description

Draws a scatterplot where each point is a circular barplot, intended to show decon results

### Usage

    florets(
      x,
      y,
      b,
      col = NULL,
      legendwindow = FALSE,
      rescale.by.sqrt = TRUE,
      border = NA,
      add = FALSE,
      cex = 1,
      bty = "n",
      xaxt = "n",
      yaxt = "n",
      xlab = "",
      ylab = "",
      ...
    )

### Arguments

`x` | Vector of x coordinates
`y` | Vector of y coordinates
`b` | matrix or cell abundances, with columns aligned with the elements of x and y
`col` | vector of colors, aligned to the rows of b.
`legendwindow` | Logical. If TRUE, the function draws a color legend in a new window
`rescale.by.sqrt` | Logical, for whether to rescale b by its square root to make value proportional to shape area, not shape length.
`border` | Color of pie segment border, defauls to NA/none
`add` | Logical. If TRUE, the function draws florets atop an existing graphics device (TRUE) or call a new device (FALSE).
`cex` | Floret size. Florets are scaled relative to the range of x and y; this further scales up or down.
`bty` | bty argument passed to plot()
`xaxt` | xaxt argument passed to plot()
`yaxt` | yaxt argument passed to plot()
`xlab` | xlab, defaults to ""
`ylab` | ylab, defaults to ""
`...` | additional arguments passed to plot()

### Value

Draws a coxcomb plot, returns no data.

### Examples

    data(mini_geomx_dataset)
    data(safeTME)
    # estimate background:
    mini_geomx_dataset$bg <- derive_GeoMx_background(
      norm = mini_geomx_dataset$normalized,
      probepool = rep(1, nrow(mini_geomx_dataset$normalized)),
      negnames = "NegProbe"
    )
    # run basic decon:
    res0 <- spatialdecon(
      norm = mini_geomx_dataset$normalized,
      bg = mini_geomx_dataset$bg,
      X = safeTME
    )
    # draw florets:
    florets(
      x = mini_geomx_dataset$annot$x,
      y = mini_geomx_dataset$annot$y,
      b = res0$beta, cex = 2
    )

[Package SpatialDecon version 1.4.3 Index]